Heng Ji

Thao Nguyen, Kuan-Hao Huang, Ge Liu et al.

We introduce Functional Group-Aware Representations for Small Molecules (FARM), a novel foundation model designed to bridge the gap between SMILES, natural language, and molecular graphs. The key idea behind FARM is the incorporation of functional group (FG) annotations at the atomic level, enabling both FG-enhanced SMILES and FG graphs. In this representation, SMILES strings are enriched with functional group information that identifies the group membership of each atom, while the FG graph captures molecular structure by representing how functional groups are connected. This tokenization injects chemical knowledge into SMILES and expands the effective molecular vocabulary, making the representation more suitable for Transformer-based models and more aligned with natural language structure. FARM learns molecular representations from two complementary perspectives to jointly encode functional and structural information. Masked language modeling on FG-enhanced SMILES captures atom-level features enriched with functional context, while graph neural networks model higher-level molecular topology through functional group connectivity. Contrastive learning is then used to align these two views into a unified embedding space, ensuring that both atom-level detail and functional group structure are jointly represented. We evaluate FARM on the MoleculeNet benchmark and achieve state-of-the-art performance on 8 out of 13 tasks. We further validate its generalization ability on a photostability dataset for quantum mechanical properties. These results demonstrate that FARM improves molecular representation learning, supports strong transfer learning across drug discovery and materials science, and enables broad applications in pharmaceutical research and functional material design.

Jiaxin Qin, Zixuan Zhang, Manling Li et al.

Extensive previous research has focused on post-training knowledge editing (KE) for language models (LMs) to ensure that knowledge remains accurate and up-to-date. One desired property and open question in KE is to let edited LMs correctly handle ripple effects, where LM is expected to answer its logically related knowledge accurately. In this paper, we answer the question of why most KE methods still create messy ripple effects. We conduct extensive analysis and identify a salient indicator, GradSim, that effectively reveals when and why updated knowledge ripples in LMs. GradSim is computed by the cosine similarity between gradients of the original fact and its related knowledge. We observe a strong positive correlation between ripple effect performance and GradSim across different LMs, KE methods, and evaluation metrics. Further investigations into three counter-intuitive failure cases (Negation, Over-Ripple, Multi-Lingual) of ripple effects demonstrate that these failures are often associated with very low GradSim. This finding validates that GradSim is an effective indicator of when knowledge ripples in LMs.

Stuti Agrawal, Nishi Uppuluri, Pranav Pillai et al.

LLM-driven dialog systems are used in a diverse set of applications, ranging from healthcare to customer service. However, given their generalization capability, it is difficult to ensure that these chatbots stay within the boundaries of the specialized domains, potentially resulting in inaccurate information and irrelevant responses. This paper introduces an unsupervised approach for automatically inducing domain-specific dialog flows that can be used to constrain LLM-based chatbots. We introduce two variants of dialog flow based on the availability of in-domain conversation instances. Through human and automatic evaluation over various dialog domains, we demonstrate that our high-quality data-guided dialog flows achieve better domain coverage, thereby overcoming the need for extensive manual crafting of such flows.

Rui Yang, Hanyang Chen, Junyu Zhang et al.

Leveraging Multi-modal Large Language Models (MLLMs) to create embodied agents offers a promising avenue for tackling real-world tasks. While language-centric embodied agents have garnered substantial attention, MLLM-based embodied agents remain underexplored due to the lack of comprehensive evaluation frameworks. To bridge this gap, we introduce EmbodiedBench, an extensive benchmark designed to evaluate vision-driven embodied agents. EmbodiedBench features: (1) a diverse set of 1,128 testing tasks across four environments, ranging from high-level semantic tasks (e.g., household) to low-level tasks involving atomic actions (e.g., navigation and manipulation); and (2) six meticulously curated subsets evaluating essential agent capabilities like commonsense reasoning, complex instruction understanding, spatial awareness, visual perception, and long-term planning. Through extensive experiments, we evaluated 24 leading proprietary and open-source MLLMs within EmbodiedBench. Our findings reveal that: MLLMs excel at high-level tasks but struggle with low-level manipulation, with the best model, GPT-4o, scoring only 28.9\% on average. EmbodiedBench provides a multifaceted standardized evaluation platform that not only highlights existing challenges but also offers valuable insights to advance MLLM-based embodied agents. Our code and dataset are available at https://embodiedbench.github.io.

Qiusi Zhan, Hyeonjeong Ha, Rui Yang et al.

Multimodal large language models (MLLMs) have advanced embodied agents by enabling direct perception, reasoning, and planning task-oriented actions from visual inputs. However, such vision driven embodied agents open a new attack surface: visual backdoor attacks, where the agent behaves normally until a visual trigger appears in the scene, then persistently executes an attacker-specified multi-step policy. We introduce BEAT, the first framework to inject such visual backdoors into MLLM-based embodied agents using objects in the environments as triggers. Unlike textual triggers, object triggers exhibit wide variation across viewpoints and lighting, making them difficult to implant reliably. BEAT addresses this challenge by (1) constructing a training set that spans diverse scenes, tasks, and trigger placements to expose agents to trigger variability, and (2) introducing a two-stage training scheme that first applies supervised fine-tuning (SFT) and then our novel Contrastive Trigger Learning (CTL). CTL formulates trigger discrimination as preference learning between trigger-present and trigger-free inputs, explicitly sharpening the decision boundaries to ensure precise backdoor activation. Across various embodied agent benchmarks and MLLMs, BEAT achieves attack success rates up to 80%, while maintaining strong benign task performance, and generalizes reliably to out-of-distribution trigger placements. Notably, compared to naive SFT, CTL boosts backdoor activation accuracy up to 39% under limited backdoor data. These findings expose a critical yet unexplored security risk in MLLM-based embodied agents, underscoring the need for robust defenses before real-world deployment.

Huimin Xu, Seungjun Yi, Terence Lim et al.

Thematic analysis (TA) is a widely used qualitative approach for uncovering latent meanings in unstructured text data. TA provides valuable insights in healthcare but is resource-intensive. Large Language Models (LLMs) have been introduced to perform TA, yet their applications in healthcare remain unexplored. Here, we propose TAMA: A Human-AI Collaborative Thematic Analysis framework using Multi-Agent LLMs for clinical interviews. We leverage the scalability and coherence of multi-agent systems through structured conversations between agents and coordinate the expertise of cardiac experts in TA. Using interview transcripts from parents of children with Anomalous Aortic Origin of a Coronary Artery (AAOCA), a rare congenital heart disease, we demonstrate that TAMA outperforms existing LLM-assisted TA approaches, achieving higher thematic hit rate, coverage, and distinctiveness. TAMA demonstrates strong potential for automated TA in clinical settings by leveraging multi-agent LLM systems with human-in-the-loop integration by enhancing quality while significantly reducing manual workload.

Dwip Dalal, Gautam Vashishtha, Utkarsh Mishra et al.

Multimodal large language models (MLLMs) often miss small details and spatial relations in cluttered scenes, leading to errors in fine-grained perceptual grounding. We introduce AttWarp, a lightweight method that allocates more resolution to query-relevant content while compressing less informative areas, all while preserving global context. At test time, the approach uses an MLLM's cross-modal attention to perform rectilinear warping of the input image, reallocating spatial resolution toward regions the model deems important, without changing model weights or architecture. This attention-guided warping preserves all original image information but redistributes it non-uniformly, so small objects and subtle relationships become easier for the same model to read while the global layout remains intact. Across five benchmarks (TextVQA, GQA, DocVQA, POPE, MMMU) and four MLLMs (LLaVA, Qwen-VL, InternVL, and InstructBLIP), AttWarp consistently improves accuracy, strengthens compositional reasoning, and reduces hallucinations, outperforming four competitive baselines that manipulate raw images at test time. Together, these results show that attention-guided warping prioritizes information relevant to the query while preserving context, and that the same MLLMs perform better when given such warped inputs.

Aditi Tiwari, Farzaneh Masoud, Dac Trong Nguyen et al.

Modern AI systems struggle most in environments where reliability is critical - scenes with smoke, poor visibility, and structural deformation. Each year, tens of thousands of firefighters are injured on duty, often due to breakdowns in situational perception. We introduce Fire360, a benchmark for evaluating perception and reasoning in safety-critical firefighting scenarios. The dataset includes 228 360-degree videos from professional training sessions under diverse conditions (e.g., low light, thermal distortion), annotated with action segments, object locations, and degradation metadata. Fire360 supports five tasks: Visual Question Answering, Temporal Action Captioning, Object Localization, Safety-Critical Reasoning, and Transformed Object Retrieval (TOR). TOR tests whether models can match pristine exemplars to fire-damaged counterparts in unpaired scenes, evaluating transformation-invariant recognition. While human experts achieve 83.5% on TOR, models like GPT-4o lag significantly, exposing failures in reasoning under degradation. By releasing Fire360 and its evaluation suite, we aim to advance models that not only see, but also remember, reason, and act under uncertainty. The dataset is available at: https://uofi.box.com/v/fire360dataset.